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-rw-r--r--gn/packages/genenetwork.scm191
1 files changed, 75 insertions, 116 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 8a76327..30f941b 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -43,7 +43,8 @@
#:use-module (gn packages python)
#:use-module (gn packages python24)
#:use-module (gn packages statistics)
- #:use-module (gn packages web))
+ #:use-module (gn packages web)
+ #:use-module (srfi srfi-1))
@@ -446,120 +447,79 @@ implemented, light on server resource usage, and fairly speedy.")
(license license:agpl3+))))
(define-public python3-genenetwork2
- (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")
- (S specification->package))
- (package
- (name "python3-genenetwork2")
- (version (string-append "2.11-guix-" (string-take commit 7) ))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git")
- ;; (url "https://github.com/genenetwork/genenetwork2_diet.git")
- (commit commit)))
- (file-name (string-append name "-" version))
- (sha256
- (base32
- "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz"))))
- (propagated-inputs
- `(;; propagated for development purposes
- ("python" ,python) ;; probably superfluous
- ("coreutils" ,coreutils)
- ("git" ,git)
- ("vim" ,vim)
- ("which" ,which)
- ("grep" ,grep)
- ("r" ,r)
- ("r-ctl" ,r-ctl)
- ; ("r-phewas" ,r-phewas)
- ("r-qtl" ,r-qtl)
- ("r-wgcna" ,r-wgcna)
- ("redis" ,redis)
- ("mariadb" ,mariadb)
- ("gemma" ,gemma-gn2)
- ("gemma-wrapper" ,gemma-wrapper)
- ("plink-ng-gn" ,plink-ng-gn)
- ("rust-qtlreaper" ,rust-qtlreaper)
- ("nginx" ,nginx)
- ("python-twint" ,python-twint)
- ("python-flask" ,python-flask)
- ("gunicorn" ,gunicorn)
- ("python-pillow" ,python-pillow)
- ;; ("python2-pil1" ,python2-pil1-gn)
- ("python2-piddle-gn" ,python2-piddle-gn) ; DEPRECATED
- ("python-cssselect" ,python-cssselect)
- ("python-elasticsearch" ,python-elasticsearch)
- ("python-htmlgen" ,python-htmlgen)
- ("python-jinja2" ,python-jinja2)
- ("python-sqlalchemy" ,python-sqlalchemy)
- ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
- ("python-setuptools" ,python-setuptools)
- ("python-scipy" ,python-scipy)
- ("python-lxml" ,python-lxml)
- ("python-mechanize" ,python-mechanize)
- ("python-mysqlclient" ,python-mysqlclient)
- ("python2-numarray" ,python2-numarray) ; DEPRECATED
- ("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-parameterized" ,python-parameterized)
- ("python-passlib" ,python-passlib)
- ("python-redis" ,python-redis)
- ("python-requests" ,python-requests)
- ("python2-rpy2" ,python2-rpy2) ; TODO
- ("python-simplejson" ,python-simplejson)
- ("python-pyyaml" ,python-pyyaml)
- ("python-unittest2" ,python-unittest2)
- ("python-xlsxwriter" ,python-xlsxwriter)
- ;; All the external js dependencies
- ("javascript-cytoscape" ,javascript-cytoscape)
- ("javascript-panzoom" ,javascript-cytoscape-panzoom)
- ("javascript-qtip" ,javascript-cytoscape-qtip)
- ("javascript-chroma" ,javascript-chroma)
- ("javascript-d3-tip" ,javascript-d3-tip)
- ("javascript-jscolor" ,javascript-jscolor)
- ("javascript-colorbox" ,javascript-colorbox)
- ("javascript-jszip" ,javascript-jszip)
- ("js-jstat" ,js-jstat)
- ("js-md5" ,js-md5)
- ("js-parsley" ,js-parsley)
- ("javascript-plotly" ,javascript-plotly)
- ("javascript-typeahead" ,javascript-typeahead)
- ("js-underscore" ,js-underscore)
- ("js-smart-time-ago" ,js-smart-time-ago)
- ("javascript-nouislider" ,javascript-nouislider)
- ("javascript-purescript-genome-browser" ,javascript-purescript-genome-browser)
- ("javascript-datatables" ,javascript-datatables)
- ("javascript-datatables-scroller" ,javascript-datatables-scroller)
- ("javascript-datatables-buttons" ,javascript-datatables-buttons)
- ("javascript-datatables-buttons-bootstrap" ,javascript-datatables-buttons-bootstrap)
- ("javascript-datatables-plugins" ,javascript-datatables-plugins)
- ("javascript-datatables-col-reorder" ,javascript-datatables-col-reorder)
- ("javascript-datatables-col-resize" ,javascript-datatables-col-resize)
- ("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles)
- ("javascript-shapiro-wilk" ,javascript-shapiro-wilk)
- ("javascript-underscore-string" ,javascript-underscore-string)
- ("javascript-qtip2" ,javascript-qtip2)
- ("javascript-d3js" ,javascript-d3js)
- ("javascript-nvd3" ,javascript-nvd3)
- ("javascript-bootstrap" ,javascript-bootstrap)
- ("javascript-jquery" ,javascript-jquery)
- ("javascript-zxcvbn-async" ,javascript-zxcvbn-async)
- ("javascript-jquery-ui" ,javascript-jquery-ui)
- ("javascript-jquery-cookie" ,javascript-jquery-cookie)
- ))
- (inputs
- `(("javascript-colorbox" ,(package-source javascript-colorbox))))
- (build-system python-build-system)
- (arguments
- `(#:python ,python-2
- #:phases
+ (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd"))
+ (package
+ (inherit genenetwork2)
+ (name "python3-genenetwork2")
+ (version (string-append "3.11-guix-" (string-take commit 7) ))
+ (propagated-inputs
+ `(,@(fold alist-delete (package-propagated-inputs genenetwork2)
+ '("python-2"
+ "python2-coverage"
+ "python2-flask"
+ "python2-gunicorn-gn"
+ "python2-cssselect"
+ "python2-elasticsearch"
+ "python2-htmlgen-gn"
+ "python2-jinja2"
+ "python2-sqlalchemy"
+ "python2-flask-sqlalchemy"
+ "python2-setuptools"
+ "python2-scipy"
+ "python2-lxml"
+ "python2-mechanize"
+ "python2-mock"
+ "python2-mysqlclient"
+ "python2-nose"
+ "python2-numarray"
+ "python2-numpy"
+ "python2-pandas"
+ "python2-parallel"
+ "python2-parameterized"
+ "python2-passlib"
+ "python2-redis"
+ "python2-requests"
+ "python2-simplejson"
+ "python2-pyyaml"
+ "python-unittest2"
+ "python2-xlsxwriter"
+ "python2-qtlreaper"))
+ ("python-pillow" ,python-pillow)
+ ("python-coverage" ,python-coverage)
+ ("python-flask" ,python-flask)
+ ("gunicorn" ,gunicorn)
+ ("python-cssselect" ,python-cssselect)
+ ("python-elasticsearch" ,python-elasticsearch)
+ ("python-htmlgen" ,python-htmlgen)
+ ("python-jinja2" ,python-jinja2)
+ ("python-sqlalchemy" ,python-sqlalchemy)
+ ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
+ ("python-setuptools" ,python-setuptools)
+ ("python-scipy" ,python-scipy)
+ ("python-lxml" ,python-lxml)
+ ("python-mechanize" ,python-mechanize)
+ ("python-mysqlclient" ,python-mysqlclient)
+ ("python-numpy" ,python-numpy)
+ ("python-pandas" ,python-pandas)
+ ("python-mock" ,python-mock)
+ ("python-parameterized" ,python-parameterized)
+ ("python-passlib" ,python-passlib)
+ ("python-redis" ,python-redis)
+ ("python-requests" ,python-requests)
+ ("python-simplejson" ,python-simplejson)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-unittest2" ,python-unittest2)
+ ("python-xlsxwriter" ,python-xlsxwriter)))
+ (arguments
+ `(#:python ,python-3
+ #:phases
(modify-phases %standard-phases
(delete 'reset-gzip-timestamps)
(add-after 'unpack 'fix-paths-scripts
(lambda _
(substitute* "bin/genenetwork2"
(("/usr/bin/env") (which "env"))
- (("python ") (string-append (which "python2") " "))
+ (("python ") (string-append (which "python") " "))
(("readlink") (which "readlink"))
(("dirname") (which "dirname"))
(("basename") (which "basename"))
@@ -581,18 +541,17 @@ implemented, light on server resource usage, and fairly speedy.")
#t)))
(add-before 'install 'fix-paths
(lambda* (#:key inputs #:allow-other-keys)
- (let* ((plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2"))
- (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")))
+ (let* (
+ (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2"))
+ (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
+ )
(substitute* '("etc/default_settings.py")
(("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
(("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))
)
))))
- #:tests? #f)) ; no 'setup.py test'
- (home-page "http://genenetwork.org/")
- (synopsis "Full genenetwork services")
- (description "Genenetwork installation sumo.")
- (license license:agpl3+))))
+ #:tests? #f)) ; no 'setup.py test'
+ )))
;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x